extension_cli: Clear out existing manifest collections for old `extension.json` (#9780)

This PR fixes an issue in the extension CLI when building extensions
using the old manifest schema (`extension.json`).

If there were values provided for the `languages`, `grammars`, or
`themes` collections, these could interfere with the packaging process.

We aren't expecting these fields to be set in the source
`extension.json` (just in the generated one), so we can clear them out
when building up the manifest.

Release Notes:

- N/A

Co-authored-by: Max <max@zed.dev>